Indian population, comprising of more than a billion people, consists of 4693 communities with several thousands of endogamous groups, 325 functioning lan-guages and 25 scripts. To address the questions related to ethnic diversity, migrations, founder populations, predisposition to complex disorders or pharmacoge-nomics, one needs to understand the diversity and relatedness at the genetic level in such a diverse popu-lation. In this backdrop, six constituent laboratories of the Council of Scientific and Industrial Research (CSIR), with funding from the Government of India, initiated a network program on predictive medicine using repeats and single nucleotide polymorphisms. The Indian Genome Variation (IGV) consortium aims to provide data on validated SNPs and repeats, both novel and reported, along with gene duplications, in over a thousand genes, in 15,000 individuals drawn from In-dian subpopulations. These genes have been selected on the basis of their relevance as functional and positional candidates in many common diseases including genes relevant to pharmacogenomics. This is the first large-scale comprehensive study of the structure of the Indian population with wide-reaching implications. A compre-hensive platform for Indian Genome Variation (IGV) data management, analysis and creation of IGVdb portal has also been developed. The samples are being collected following ethical guidelines of Indian Council of Medical Research (ICMR) and Department of Bio-technology (DBT), India. This paper reveals the struc-ture of the IGV project highlighting its various aspects like genesis, objectives, strategies for selection of genes, identification of the Indian subpopulations, collection of samples and discovery and validation of genetic mark-ers, data analysis and monitoring as well as the project's data release policy. Keywords Indian population AE Ethnicity AE Genetic structure AE Single nucleotide polymorphism AE Repeat polymorphism AE Indian genome variation database Introduction